Identifying G-protein coupled receptors using weighted Levenshtein distance and the nearest neighbor method

G-protein coupled receptors （GPCRs） are a class of seven-helix transmembrane proteins that have been used in bioinformatics as the targets to facilitate drug discovery for human diseases. Although thousands of GPCR sequences have been collected, the ligand specificity of many GPCRs is still unknown and only one crystal structure of the rhodopsin-like family has been solved. Therefore, identifying GPCR types only from sequence data has become an important research issue. In this study, a novel technique for identifying GPCR types based on the weighted Levenshtein distance between two receptor sequences and the nearest neighbor method （NNM） is introduced, which can deal with receptor sequences with different lengths directly. In our experiments for classifying four classes （acetylcholine, adrenoceptor, dopamine, and serotonin） of the rhodopsin-like family of GPCRs, the error rates from the leave-one-out procedure and the leave-half-out procedure were 0.62% and 1.24%, respectively. These results are prior to those of the covariant discriminant algorithm, the support vector machine method, and the NNM with Euclidean distance.     

磷脂酰丝氨酸合成酶基因的克隆及在枯草芽孢杆菌中的表达

应用 PCR技术从 Escherichia coli K12 Sgal- (ExPASy P23830) 中扩增到大小为 1350bp编码磷脂酰丝氨酸合成酶的 DNA片段,将其插入枯草芽孢杆菌诱导型表达载体 pBES,获得重组质粒 pBES-pss后转化 Bacillus subtilis DB104。经蔗糖诱导后,该磷脂酰丝氨酸合成酶在 Bacillus subtilis DB104 (pBES-pss)中获得胞外分泌表达,SDS-PAGE分析发现目的蛋白分子量约为 52kDa,酶联比色法检测酶活力为 1.50U/mL,提高了磷脂酰丝氨酸合成酶的表达产量,为工业化发酵生产磷脂酰丝氨酸合成酶奠定了良好的基础。     

Optimizing medium constituents and fermentation conditions for citric acid production from palmyra jaggery using response surface method

The quantitative effects of pH, temperature, time of fermentation, sugar concentration, nitrogen concentration and potassium ferrocyanide on citric acid production were investigated using a statistical experimental design. It was found that palmyra jaggery (sugar syrup from the palmyra palm) is a suitable substrate for increasing the yield of citric acid using Aspergillus niger MTCC 281 by submerged fermentation. Regression equations were used to model the fermentation in order to determine optimum fermentation conditions. Higher yields were obtained after optimizing media components and conditions of fermentation. Maximum citric acid production was obtained at pH 5.35, 29.76 °C, 5.7 days of fermentation with 221.66 g of substrate/l, 0.479 g of ammonium nitrate/l and 2.33 g of potassium ferrocyanide/l.     

利用反硝化细菌法测试水体硝酸盐氮氧同位素

反硝化细菌方法作为测试硝酸盐氮氧同位素组成的最新方法,具有可测试低浓度水样、对样品无需特殊处理、不会交叉污染和需样量少等诸多优点而得到迅速发展。本研究率先在国内实验室利用反硝化细菌法成功测试了硝酸盐氮氧同位素组成,将经过5～10d培养的反硝化细菌Pseudomonas aureofaciens离心,然后将菌液浓缩5倍,再向顶空进样瓶注入3mL菌液,密封后利用高纯氮气吹扫3h以上,注入50nmolNO3-水样经过夜培养灭活后,使用TraceGasPre-concentrator-Isoprime测试N2O同位素组成,结果表明,重现性和测试精度与国际上类似研究接近。该方法的建立对于国内开展河流及湖泊(水库)、降水等氮的生物地球化学循环将起到促进作用。     

米槠和杉木人工林土壤呼吸及其组分分析

区分森林土壤呼吸组分是了解生态系统碳循环的重要环节。该文以福建省三明市格氏栲自然保护区米槠(Castanopsis carlesii)人工林和邻近的杉木(Cunninghamia lanceolata)人工林为研究对象, 于2012年8月至2013年7月, 采用LI-8100开路式土壤碳通量系统, 通过挖壕沟方法, 测定了土壤呼吸及异养呼吸的速率, 同时测定了5 cm深处的土壤温度和0-12 cm深处的土壤含水量。利用指数模型和双因素模型, 分析土壤呼吸及其组分与土壤温度和土壤含水量的关系, 同时计算了土壤呼吸各组分在土壤呼吸中所占的比例, 并分析了不同森林类型对土壤呼吸及其组分的影响。结果表明: 米槠人工林和杉木人工林土壤呼吸及其组分的季节变化显著, 均呈单峰型曲线, 与5 cm深处的土壤温度呈极显著正相关关系。土壤温度可以分别解释米槠人工林土壤呼吸、自养呼吸和异养呼吸变化的70.3%、73.4%和58.2%, 可以解释杉木人工林土壤呼吸、自养呼吸和异养呼吸变化的77.9%、65.7%和79.2%。土壤呼吸及其组分与土壤含水量没有相关关系。米槠和杉木人工林自养呼吸的年通量分别为4.00和2.18 t C·hm^-2·a^-1, 占土壤呼吸年通量的32.5%和24.1%; 异养呼吸年通量分别为8.32和6.88 t C·hm^-2·a^-1, 分别占土壤呼吸年通量的67.5%和75.9%, 米槠人工林土壤呼吸及其组分的年通量都大于杉木人工林。     

猕猴桃属十个种的染色体倍性鉴定

猕猴桃属(Actinidia)植物全世界有66种,约有118个种下分类单位(也有新的划分方法将其划分为54种21变种),其中大部分为中国特有。在猕猴桃杂交育种中,不同倍性之间选配不当会出现杂交失败、后代不育等现象,因此倍性鉴定是猕猴桃常规育种亲本选择的前提条件之一。但到目前为止,不少猕猴桃种或亚种的染色体倍性研究并不十分清楚,因而限制了这些资源的进一步开发利用。该研究针对广西植物研究所猕猴桃种质资源圃收集的目前倍性尚不明确的白萼、白花柱果、二色花、临桂、卵圆叶、桃花、宛田、长果、融水和五瓣猕猴桃等10个种类的猕猴桃,使用酸解法制备染色体标本,通过显微镜观察确定其倍性。这10个种类大多为广西特有,其中蕴藏着独特的优良园艺性状,具有很高的生产和开发价值。该研究结果表明这10个种类猕猴桃的染色体倍性均为二倍体(2n=2x=58)。该研究结果进一步丰富了猕猴桃种质资源多样性数据库,为这些猕猴桃资源的合理开发利用奠定了基础。     

耕作方法和除草剂对玉米田杂草群落的影响

应用群落生态学方法,在中国科学院沈阳生态实验站对玉米田杂草群落进行了调查研究,探讨了耕作方法和除草剂对杂草群落组成、多样性和生物量的影响.结果表明,玉米田优势种杂草为野黍、苘麻、大狼把草和鸭趾草,其中野黍重要值最高;免耕不施加除草剂处理6月下旬杂草生物量较大,5月末到8月中旬物种丰富度较高(S),7月1日和8月1日均匀度(J)较低,优势集中性(C)较高,均与常规施加除草剂处理有显著差异.施用除草剂可减少免耕玉米田杂草种类,抑制杂草生物量的增长.耕作方法和除草剂可对杂草群落组成、多样性及稳定性产生影响.     

Development of thermodynamic optimum searching (TOS) to improve the prediction accuracy of flux balance analysis

Flux balance analysis (FBA) has been widely used in calculating steady‐state flux distributions that provide important information for metabolic engineering. Several thermodynamics‐based methods, for example, quantitative assignment of reaction directionality and energy balance analysis have been developed to improve the prediction accuracy of FBA. However, these methods can only generate a thermodynamically feasible range, rather than the most thermodynamically favorable solution. We therefore developed a novel optimization method termed as thermodynamic optimum searching (TOS) to calculate the thermodynamically optimal solution, based on the second law of thermodynamics, the minimum magnitude of the Gibbs free energy change and the maximum entropy production principle (MEPP). Then, TOS was applied to five physiological conditions of Escherichia coli to evaluate its effectiveness. The resulting prediction accuracy was found significantly improved (10.7–48.5%) by comparing with the ¹³C‐fluxome data, indicating that TOS can be considered an advanced calculation and prediction tool in metabolic engineering. Biotechnol. Bioeng. 2013; 110: 914–923. © 2012 Wiley Periodicals, Inc.     

Ethanol production from rice hull using Pichia stipitis and optimization of acid pretreatment and detoxification processes

The goal of this study was to produce ethanol from rice hull hydrolysates (RHHs) using Pichia stipitis strains and to optimize dilute acid hydrolysis and detoxification processes by response surface methodology (RSM). The optimized conditions were found as 127.14°C, solid:liquid ratio of 1:10.44 (w/v), acid ratio of 2.52% (w/v), and hydrolysis time of 22.01 min. At these conditions, the fermentable sugar concentration was 21.87 g/L. Additionally, the nondetoxified RHH at optimized conditions contained 865.2 mg/L phenolics, 24.06 g/L fermentable sugar, no hydroxymethylfurfural (HMF), 1.62 g/L acetate, 0.36 g/L lactate, 1.89 g/L glucose, and 13.49 g/L fructose + xylose. Furthermore, RHH was detoxified with various methods and the best procedures were found to be neutralization with CaO or charcoal treatment in terms of the reduction of inhibitory compounds as compared to nondetoxified RHH. After detoxification procedures, the content of hydrolysates consisted of 557.2 and 203.1 mg/L phenolics, 19.7 and 21.60 g/L fermentable sugar, no HMF, 0.98 and 1.39 g/L acetate, 0 and 0.04 g/L lactate, 1.13 and 1.03 g/L glucose, and 8.46 and 12.09 g/L fructose + xylose, respectively. Moreover, the base‐line mediums (control), and nondetoxified and detoxified hydrolysates were used to produce ethanol by using P. stipitis strains. The highest yields except that of base‐line mediums were achieved using neutralization (35.69 and 38.33% by P. stipitis ATCC 58784 and ATCC 58785, respectively) and charcoal (37.55% by P. stipitis ATCC 58785) detoxification methods. Results showed that the rice hull can be utilized as a good feedstock for ethanol production using P. stipitis. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:872–882, 2016     

根癌农杆菌介导AtNHX1基因转化番茄的研究

构建AtNHX1基因植物表达载体,通过农杆菌介导法将其转入番茄。探讨了外植体类型、农杆菌菌株和不同筛选标记对芽诱导分化的影响。对抗性植株进行PCR检测,获得15株转基因植株。对转基因番茄T1代进行80mmol/LNaHCO胁迫处理,转基因植株的相对生长量高于对照植株,显示AtNHX1基因的导入提高了番茄对碱性盐的耐受性。